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A computationally efficient mode space simulation method for atomistic simulation of a graphene nanoribbon field-effect transistor in the ballistic limits is developed. The proposed simulation scheme, which solves the nonequilibrium Green’s function coupled with a three dimensional Poisson equation, is based on the atomistic Hamiltonian in a decoupled mode space. The mode space approach, which only treats a few modes (subbands), significantly reduces the simulation time. Additionally, the edge bond relaxation and the third nearest neighbor effects are also included in the quantum transport solver. Simulation examples show that the mode space approach can significantly decrease the simulation cost by about an order of magnitude, yet the results are still accurate. This article also demonstrates that the effects of the edge bond relaxation and the third nearest neighbor significantly influence the transistor’s performance and are necessary to be included in the modeling.